title: Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline.
abstract: RNA-seq experiments are now routinely used for the large scale sequencing of transcripts. In bacteria or archaea, such deep sequencing experiments typically produce 10-50 million fragments that cover most of the genome, including intergenic regions. In this context, the precise delineation of the non-coding elements is challenging. Non-coding elements include untranslated regions (UTRs) of mRNAs, independent small RNA genes (sRNAs) and transcripts produced from the antisense strand of genes (asRNA). Here we present a computational pipeline (DETR'PROK: detection of ncRNAs in prokaryotes) based on the Galaxy framework that takes as input a mapping of deep sequencing reads and performs successive steps of clustering, comparison with existing annotation and identification of transcribed non-coding fragments classified into putative 5' UTRs, sRNAs and asRNAs. We provide a step-by-step description of the protocol using real-life example data sets from Vibrio splendidus and Escherichia coli.
authors.affiliation: Université Paris-Sud, Institut de Génétique et Microbiologie, CNRS UMR 8621, Orsay F-91405, France.
authors.forename: Claire
authors.initials: C
authors.lastname: Toffano-Nioche
authors.forename: Yufei
authors.initials: Y
authors.lastname: Luo
authors.forename: Claire
authors.initials: C
authors.lastname: Kuchly
authors.forename: Claire
authors.initials: C
authors.lastname: Wallon
authors.forename: Delphine
authors.initials: D
authors.lastname: Steinbach
authors.forename: Matthias
authors.initials: M
authors.lastname: Zytnicki
authors.forename: Annick
authors.initials: A
authors.lastname: Jacq
authors.forename: Daniel
authors.initials: D
authors.lastname: Gautheret
mesh_terms: D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D012333:RNA, Messenger / Q000235:genetics / Q000302:isolation & purification*; D022661:RNA, Untranslated / Q000235:genetics / Q000302:isolation & purification*
chemical_list: D012333:RNA, Messenger; D022661:RNA, Untranslated
keywords: Antisense RNA; Archaea; Bacteria; Non-coding RNA; Small RNA; Untranslated regions